On Tue, Mar 01, 2016, Arati Paudyal wrote:
>
> I am trying to get the ras-raf tutorial work for the MMPBSA tutorial. And
> basically I am having problem at the very first minimization step.
> Initially I used maxcyc=1000 and ncyc=500 and I kept getting " ...
> RESTARTED DUE TO LINMIN FAILURE ...
You will always get this sort of error if you turn shake on with minimization,
i.e. have ntc=2.
Basically, most Amber users just use minimization to remove bad initial
contacts (with, say, a few hundred steps of minimization). After that, MD
equilibration can be used to prepare the system.
If you really need to get to true minima, especially with SHAKE, you will
need to use NAB. There is a learning curve there (not *too* steep), so be
sure this is something you really need to do.
....dac
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Received on Tue Mar 01 2016 - 18:00:03 PST
